Knottsberry Farm the amusement park? Is a couple hours north os San Diego. When aremyou coming to San Diego? I would put Wild Animal Park on your to do list. Are you into wine? There are some wineries in the the surrounding area.
Agree about Knott's being a haul from SD -- especially in traffic (unless you have a lot of time and are in to rollercoasters, I'd skip it; if you really want to do a So Cal amusement park, I'd choose the Disneyland Resort over Knott's, but I probably wouldn't do either for a honeymoon). There is so much to do in SD (and, it's pretty spread out, so you'll want to plan an itinerary so you're not backtracking in traffic -- which can be heavy), some of our favorites: USS Midway, all of Balboa park (where the zoo is located) -- tons of museums and beautiful gardens, kayaking from the La Jolla caves, the Scripps aquarium, Carlsbad is a cute beach town (but there are tons of others as well), do a hot air balloon trip out of Del Mar, Sea World, Mission Bay, I agree about the Safari Park and wineries (both on the Eastern side of the county). You can definitely keep busy for a good week.
Knott's Berry Farm is up by where I live, it's close to Disneyland and is a very long drive just so you're aware. And with all of the road construction they're doing lately, it's likely to be worse than normal.
San Diego Zoo is amazing and if you have the time you should check out the Safari Park too. It's completely different and in my opinion way better than the zoo.
Definitely check out the Gaslamp District for food and bars if you want a bit night life. There are nice wineries down there and if you feel like a drive out to Temecula you'll find even better wineries.
But there are so many museums in San Diego you'll easily be busy the whole time if you choose to
Knottsberry Farm is a little far from downtown San Diego. You are closer to Seaworld & Legoland, and Disneyland even (I think). I would plan some time to spend at the beach, that's always fun. Gaslamp is a fun place to walk around especially at night, lots of restaurants & shops. You could go to a Padres game depending on when you go. You could also look into driving to Coronado (great beaches & the Hotel Del is beautiful) or a boat ride to Catalina. La Jolla has some great coves for diving & kayaking!
Petco Park! My fiance works there and it is a beautiful park. Also just exploring San Diego is amazing-- rent a couple of the scooters and just ride around during the weekend-- you will see some fun stuff!